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(-) Description

Title :  SOLUTION STRUCTURE OF THE RBCC/TRIM B-BOX1 DOMAIN OF HUMAN MID1: B-BOX WITH A RING
 
Authors :  M. A. Massiah, B. N. Simmons, K. M. Short, T. C. Cox
Date :  20 Dec 05  (Deposition) - 09 May 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (13x)
Keywords :  B-Box, Mid1, Ring Finger, Zinc-Finger, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Massiah, B. N. Simmons, K. M. Short, T. C. Cox
Solution Structure Of The Rbcc/Trim B-Box1 Domain Of Human Mid1: B-Box With A Ring.
J. Mol. Biol. V. 358 532 2006
PubMed-ID: 16529770  |  Reference-DOI: 10.1016/J.JMB.2006.02.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MIDLINE-1
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T2
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentB-BOX 1 DOMAIN (RESIDUES: 87 - 164)
    GeneMID1, FXY, RNF59, TRIM18, XPRF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRIPARTITE MOTIF PROTEIN 18, PUTATIVE TRANSCRIPTION FACTOR XPRF, MIDIN, RING FINGER PROTEIN 59

 Structural Features

(-) Chains, Units

  
NMR Structure (13x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:119 , CYS A:122 , CYS A:142 , CYS A:145BINDING SITE FOR RESIDUE ZN A 200
2AC2SOFTWARECYS A:134 , CYS A:137 , HIS A:150 , HIS A:159BINDING SITE FOR RESIDUE ZN A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FFW)

(-) Cis Peptide Bonds  (2, 26)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13Asp A:125 -Pro A:126
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13Lys A:154 -Pro A:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FFW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FFW)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003807871aENSE00001486317X:10851773-10851673101TRI18_HUMAN-00--
1.6cENST000003807876cENSE00001276841X:10535643-10534928716TRI18_HUMAN1-2202201A:87-16478
1.7ENST000003807877ENSE00001195785X:10491227-1049113296TRI18_HUMAN221-252320--
1.8ENST000003807878ENSE00000854562X:10463731-10463624108TRI18_HUMAN253-288360--
1.9ENST000003807879ENSE00000665015X:10450668-10450520149TRI18_HUMAN289-338500--
1.10ENST0000038078710ENSE00000665013X:10442790-10442663128TRI18_HUMAN338-381440--
1.11ENST0000038078711ENSE00001661606X:10437880-10437737144TRI18_HUMAN381-429490--
1.12bENST0000038078712bENSE00001142388X:10427847-10427686162TRI18_HUMAN429-483550--
1.13bENST0000038078713bENSE00000665007X:10423117-10422910208TRI18_HUMAN483-552700--
1.14bENST0000038078714bENSE00001486255X:10417756-104135964161TRI18_HUMAN552-6671160--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:78
 aligned with TRI18_HUMAN | O15344 from UniProtKB/Swiss-Prot  Length:667

    Alignment length:78
                                    96       106       116       126       136       146       156        
          TRI18_HUMAN    87 QKASVSGPNSPSETRRERAFDANTMTSAEKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRLIEP 164
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............................................eee....eeehhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.6c  PDB: A:87-164 UniProt: 1-220 [INCOMPLETE]                           Transcript 1
                 2ffw A  87 QKASVSGPNSPSETRRERAFDANTMTSAEKVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRLIEP 164
                                    96       106       116       126       136       146       156        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2FFW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FFW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FFW)

(-) Gene Ontology  (25, 25)

NMR Structure(hide GO term definitions)
Chain A   (TRI18_HUMAN | O15344)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    GO:0007026    negative regulation of microtubule depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol.
    GO:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    GO:0032874    positive regulation of stress-activated MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0035372    protein localization to microtubule    A process in which a protein is transported to, or maintained at, a microtubule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        TRI18_HUMAN | O153442dq5 2jun 5im8

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